[gmx-users] extracting water molecules from trajectory

T.A.Wassenaar at chem.rug.nl T.A.Wassenaar at chem.rug.nl
Sun May 23 12:28:25 CEST 2004


Hi Kay,

Actually, I've got a modified versions of src/gmxlib/pbc.c and
src/tools/trjconv.c which do just that; adding the distance from one group
to the other to the b-factor field. I can mail you the sources a bit later
(that is, when I'm on the lab again and I haven't forgotten). In case it
slips my mind :S send me a reminder...

Cheers,

Tsjerk


 On Wed, 19 May 2004, Kay Gottschalk wrote:

> thanks, works:) Would be neat to have the protein-water distance as  
> b-factor in the output-pdb - where would I have to change things to get  
> that done?
> Cheers,
> K.
> 
> On May 19, 2004, at 5:15 PM, David van der Spoel wrote:
> 
> > On Wed, 2004-05-19 at 15:58, Kay Gottschalk wrote:
> >> Hi all,
> >>
> >> I recently read something in the discussion list about extracting  
> >> water
> >> from a trajectory that is in a certain distance to the protein.
> >> Unfortunately I can't find it anymore. Could you please update me on
> >> how to do that?
> > trjorder
> >> Thanks,
> >> K.
> >>
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> > --  
> > David.
> > _______________________________________________________________________ 
> > _
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone:  +46 18 471 4205  fax: +46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org    
> > http://xray.bmc.uu.se/~spoel
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